Data requests

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How to request data/analyses

Guillaume set up trac, a system for tracking requests for data and analyses. Please use this system for data requests from now on.

You can access this program at this address : User name : iseem password : daffodil

It is currently set up with a common username for everyone due to security concerns. There are a couple functionalities that may not apply to us so feel free to overlook those.

The two main options for everyone is : View Tickets and New Ticket (after you log in). The one thing I want to point your attention towards is the "Assign to" text box for creating tickets. Please write the name of the person opening the ticket in that field so I can tell who is opening what ticket. It'll be a lot easier for me to keep track of things.

Request List from Dec 09 Meeting

  • Josh
    • OTUs - from rRNA - from ocean PCR and metagenomic data
    • OPFs from metagenomic data
  • James
    • OTUs filtered by narrower taxonomic range (e.g. families)
    • OTUs from both metagenomic and additional ocean PCR data
  • Sam
    • Protein families
      • alignments, trees from metagenomic data for those families
    • Simulations
      • Generating and analyzing trees from simulated data
  • Tom
    • All vs. all clustering of protein sequences from whole genome data
      • Build the families
  • Dongying
    • Merge families from different phyla
      • MySQL database of relationships between taxonomy and sequences (map JGI <-> MicrobeDB?)
    • Install HMMER3 in centralized location
      • Get consensus sequences for HMM profiles to group HMMs/families into clusters
  • Morgan
    • All vs. all BLASTs
    • Access to many metagenomic data sets with metadata (grab from CAMERA)?
  • Steve
    • Alignments of metagenomic reads to more gene families (using AMPHORA?)
      • For GOS data set
      • Additional marker gene families from Dongying
      • Additional markers for different taxonomic groups (archaea, Actinos, etc.)